1RK2
E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1RKD | 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.8 | CRYSTALS WERE GROWN IN THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4 AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS- HCL BUFFERED TO PH 4.8. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 33.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.201 | α = 90 |
b = 62.492 | β = 90 |
c = 337.8 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | BENT MIRROR | 1998-05-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.25 | 13 | 99.1 | 0.072 | 17 | 4 | 55979 | 26 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.25 | 2.29 | 98.8 | 0.291 | 3.9 | 4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309 | 2.25 | 13 | 55979 | 2815 | 99 | 0.228 | 0.265 | RANDOM | 24.4 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.63 | 5.01 | -6.64 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.4 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.81 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8972 |
Nucleic Acid Atoms | |
Solvent Atoms | 409 |
Heterogen Atoms | 172 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |